Skip to content
Permalink
Branch: master
Find file Copy path
Find file Copy path
Fetching contributors…
Cannot retrieve contributors at this time
executable file 443 lines (338 sloc) 26.9 KB
title layout active
Export
default
export

Audience and Scope

This implementation guide is intended to be used by developers of backend services (clients) and FHIR Resource Servers (e.g., EHR systems, data warehouses, and other clinical and administrative systems) that aim to interoperate by sharing large FHIR datasets. The guide defines the application programming interfaces (APIs) through which an authenticated and authorized client may request a bulk-data export from a server, receive status information regarding progress in the generation of the requested files, and retrieve these files. It also includes recommendations regarding the FHIR resources that might be exposed through the export interface.

The scope of this document does NOT include:

  • A legal framework for sharing data between partners, including Business Associate Agreements, Service Level Agreements, and Data Use Agreements
  • Real-time data exchange
  • Data transformations that may be required by the client
  • Patient matching (although identifiers may be included in the exported FHIR resources)
  • Management of FHIR groups (although some bulk data operations require a FHIR Group id, this guide does not specify how Group resources are created and maintained within a system)

Underlying Standards

Terminology

This profile inherits terminology from the standards referenced above. The key words "REQUIRED", "SHALL", "SHALL NOT", "SHOULD", "SHOULD NOT", "RECOMMENDED", "MAY", and "OPTIONAL" in this specification are to be interpreted as described in RFC2119.

Security Considerations

All exchanges described herein between a client and a server SHALL be secured using Transport Layer Security (TLS) Protocol Version 1.2 (RFC5246) or a more recent version of TLS. Use of mutual TLS is OPTIONAL.

With each of the requests described herein, implementers are encouraged to implement OAuth 2.0 access management in accordance with the SMART Backend Services: Authorization Guide. Implementations MAY include non-RESTful services that use authorization schemes other than OAuth 2.0, such as mutual-TLS or signed URLs.

This implementation guide does not address protection of the servers themselves from potential compromise. An adversary who successfully captures administrative rights to a server will have full control over that server and can use those rights to undermine the server's security protections. In the bulk-data-export workflow, the file server will be a particularly attractive target, as it holds highly sensitive and valued PHI. An adversary who successfully takes control of a file server may choose to continue to deliver files in response to client requests, so that neither the client nor the FHIR server is aware of the take-over. Meanwhile, the adversary is able to put the PHI to use for its own devious purposes.

Healthcare organizations have an imperative to protect PHI persisted in file servers in both cloud and data-center environments. A range of existing and emerging approaches can be used to accomplish this, not all of which would be visible at the API level. This specification does not dictate a particular approach at this time, though it does support the use of an “Expires” header to limit the time period a file will be available for client download (removal of the file from the server is left up to the implementer). We recommend that servers SHOULD not delete files from a bulk data response that a client is actively in the process of downloading regardless of the pre-specified Expires time. Work currently underway is exploring possible approaches for protecting extracted files persisted in the file server.

Data access control obligations can be met with a combination of in-band restrictions such as OAuth scopes, and out-of-band restrictions, where servers limit the data returned to a specific client in accordance with local considerations (e.g. policies or regulations). For example, some clients are authorized to access sensitive mental health information and some aren't; this authorization is defined out-of-band, but when a client requests a full data set, filtering is automatically applied by the server, restricting the data that the client receives.

Bulk data export can be a resource-intensive operation. Server developers should consider and mitigate the risk of intentional or inadvertent denial-of-service attacks (though the details are beyond the scope of this specification).

Request Flow

Bulk Data Kick-off Request

This FHIR Operation initiates the asynchronous generation of data to which the client is authorized -- whether that be all patients, a subset (defined group) of patients, or all available data contained in a FHIR server.

The FHIR server SHALL limit the data returned to only those FHIR resources for which the client is authorized.

The FHIR server SHALL support invocation of this operation using the FHIR Asynchronous Request Pattern.

For Patient- and Group-level requests requests, the Patient Compartment SHOULD be used as a point of reference for recommended resources to be returned. However, other resources outside of the patient compartment that are helpful in interpreting the patient data (such as Organization and Practitioner) may also be returned.

Endpoint - All Patients

GET [fhir base]/Patient/$export

View table of parameters for Patient Export

FHIR Operation to obtain a detailed set of FHIR resources of diverse resource types pertaining to all patients.

Endpoint - Group of Patients

GET [fhir base]/Group/[id]/$export

View table of parameters for Group Export

FHIR Operation to obtain a detailed set of FHIR resources of diverse resource types pertaining to all patients in specified Group.

If a FHIR server supports Group-level data export, it SHOULD support reading and searching for Group resource. This enables clients to discover available groups based on stable characteristics such as Group.identifier.

Note: How these Groups are defined is specific to each FHIR system's implementation. For example, a payer may send a healthcare institution a roster file that can be imported into their EHR to create or update a FHIR group. Group membership could be based upon explicit attributes of the patient, such as age, sex or a particular condition such as PTSD or Chronic Opioid use, or on more complex attributes, such as a recent inpatient discharge or membership in the population used to calculate a quality measure. FHIR-based group management is out of scope for the current version of this implementation guide.

Endpoint - System Level Export

GET [fhir base]/$export

View table of parameters for Export

Export data from a FHIR server, whether or not it is associated with a patient. This supports use cases like backing up a server, or exporting terminology data by restricting the resources returned using the _type parameter.

Headers

  • Accept (string, required)

    Specifies the format of the optional OperationOutcome resource response to the kick-off request. Currently, only application/fhir+json is supported.

  • Prefer (string, required)

    Specifies whether the response is immediate or asynchronous. The header SHALL be set to respond-async https://tools.ietf.org/html/rfc7240.

Query Parameters

Query Parameter Optionality Type Description
_outputFormat optional String The format for the requested bulk data files to be generated as per [FHIR Asynchronous Request Pattern](http://hl7.org/fhir/async.html). Defaults to application/fhir+ndjson. Servers SHALL support [Newline Delimited JSON](http://ndjson.org), but MAY choose to support additional output formats. Servers SHALL accept the full content type of application/fhir+ndjson as well as the abbreviated representations application/ndjson and ndjson.
_since optional FHIR instant Resources will be included in the response if their state has changed after the supplied time (e.g. if Resource.meta.lastUpdated is later than the supplied _since time).
_type optional string of comma-delimited FHIR resource types Only resources of the specified resource types(s) SHALL be included in the response. If this parameter is omitted, the server SHALL return all supported resources within the scope of the client authorization. For Patient- and Group-level requests, the Patient Compartment SHOULD be used as a point of reference for recommended resources to be returned. However, other resources outside of the patient compartment that are helpful in interpreting the patient data (such as Organization and Practitioner) may also be returned. Servers unable to support _type SHOULD return an error and OperationOutcome resource so clients can re-submit a request omitting the _type parameter.

Resource references MAY be relative URLs with the format <resource type>/<id>, or absolute URLs with the same structure rooted in the base URL for the server from which the export was performed. References will be resolved by looking for a resource with the specified type and id within the file set.

For example _type=Practitioner could be used to bulk data extract all Practitioner resources from a FHIR endpoint.

Note: Implementations MAY limit the resources returned to specific subsets of FHIR, such as those defined in the Argonaut Implementation Guide. If the client explicitly asks for export of resources that the bulk data server doesn't support, the server SHOULD return details via an OperationOutcome resource in an error response to the request.

Experimental Query Parameters

As a community, we've identified use cases for finer-grained, client-specified filtering. For example, some clients may want to retrieve only active prescriptions (rather than historical prescriptions), or only laboratory observations (rather than all observations). We have considered several approaches to finer-grained filtering, including FHIR's GraphDefinition, the Clinical Quality Language (CQL), and FHIR's REST API search parameters. We expect this will be an area of active exploration, so for the time being this implementation guide defines an experimental syntax based on search parameters that works side-by-side with the coarse-grained _type-based filtering.

To request finer-grained filtering, a client MAY supply a _typeFilter parameter alongside the _type parameter. The value of the _typeFilter parameter is a comma-separated list of FHIR REST API queries that further restrict the results of the query. Servers MAY further limit the data returned to a specific client in accordance with local considerations (e.g. policies or regulations). Understanding _typeFilter is OPTIONAL for FHIR servers; clients SHOULD be robust to servers that ignore _typeFilter.

Note for client developers: Because both _typeFilter and _since can restrict the results returned, the interaction of these parameters may be surprising. Think carefully through the implications when constructing a query with both of these parameters. As the _typeFilter is experimental and optional, we have not yet determined expectation for _include, _revinclude, or support for any specific search parameters.

Example Request with _typeFilter

The following is an export request for MedicationRequest resources and Condition resources, where the client would further like to restrict MedicationRequests to requests that are active, or else completed after July 1, 2018. This can be accomplished with two subqueries joined together with a comma for a logical "or":

  • MedicationRequest?status=active
  • MedicationRequest?status=completed&date=gt2018-07-01T00:00:00Z

To create a _typeFilter parameter, a client should URL encode these two subqueries and join them with ,. Newlines and spaces have been added for clarity, and would not be included in a real request:

$export?
  _type=
    MedicationRequest,
    Condition&
  _typeFilter=
    MedicationRequest%3Fstatus%3Dactive,
    MedicationRequest%3Fstatus%3Dcompleted%26date%3Dgt2018-07-01T00%3A00%3A00Z

Note: The Condition resource is included in _type but omitted from _typeFilter because the client intends to request all Condition resources without any filters.

Response - Success

  • HTTP Status Code of 202 Accepted
  • Content-Location header with the absolute URL of an endpoint for subsequent status requests (polling location)
  • Optionally, a FHIR OperationOutcome resource in the body

Response - Error (e.g., unsupported search parameter)

  • HTTP Status Code of 4XX or 5XX
  • The body SHALL be a FHIR OperationOutcome resource in JSON format

If a server wants to prevent a client from beginning a new export before an in-progress export is completed, it SHOULD respond with a 429 Too Many Requests status and a Retry-After header, following the rate-limiting advice for "Bulk Data Status Request" below.


Bulk Data Delete Request

After a bulk data request has been started, a client MAY send a delete request to the URL provided in the Content-Location header to cancel the request.

Endpoint

DELETE [polling content location]

Response - Success

  • HTTP Status Code of 202 Accepted
  • Optionally a FHIR OperationOutcome resource in the body

Response - Error Status

  • HTTP status code of 4XX or 5XX
  • The body SHALL be a FHIR OperationOutcome resource in JSON format

Bulk Data Status Request

After a bulk data request has been started, the client MAY poll the status URL provided in the Content-Location header.

Clients SHOULD follow an exponential backoff approach when polling for status. Servers SHOULD supply a Retry-After header with a http date or a delay time in seconds. When provided, clients SHOULD use this information to inform the timing of future polling requests. Servers SHOULD keep an accounting of status queries received from a given client, and if a client is polling too frequently, the server SHOULD respond with a 429 Too Many Requests status code in addition to a Retry-After header, and optionally a FHIR OperationOutcome resource with further explanation. If excessively frequent status queries persist, the server MAY return a 429 Too Many Requests status code and terminate the session. Other standard HTTP 4XX as well as 5XX status codes may be used to identify errors as mentioned.

When requesting status, the client SHOULD use an Accept header indicating a content type of application/json. In the case that errors prevent the export from completing, the server SHOULD respond with a FHIR OperationOutcome resource in JSON format.

Endpoint

GET [polling content location]

Responses

Response Type Description Example Response Headers + Body
In-Progress Returned by the server while it is processing the $export request.
Status: 202 Accepted
X-Progress: “50% complete”
Retry-After: 120
Error Returned by the server if the export operation fails.
Status: 500 Internal Server Error
Content-Type: application/json

{  "resourceType": "OperationOutcome",  "id": "1",  "issue": [   {    "severity": "error",    "code": "processing",    "details": {     "text": "An internal timeout has occurred"    }   }  ] }

Complete Returned by the server when the export operation has completed.
Status: 200 OK
Expires: Mon, 22 Jul 2019 23:59:59 GMT
Content-Type: application/json

{  "transactionTime": "[instant]",  "request" : "[base]/Patient/$export?_type=Patient,Observation",  "requiresAccessToken" : true,  "output" : [{   "type" : "Patient",   "url" : "http://serverpath2/patient_file_1.ndjson"  },{   "type" : "Patient",   "url" : "http://serverpath2/patient_file_2.ndjson"  },{   "type" : "Observation",   "url" : "http://serverpath2/observation_file_1.ndjson"  }],  "error" : [{   "type" : "OperationOutcome",   "url" : "http://serverpath2/err_file_1.ndjson"  }],  "extension":{"http://myserver.example.org/extra-property": true} }

Response - In-Progress Status

  • HTTP Status Code of 202 Accepted
  • Optionally, the server MAY return an X-Progress header with a text description of the status of the request that's less than 100 characters. The format of this description is at the server's discretion and may be a percentage complete value, or a more general status such as "in progress". The client MAY parse the description, display it to the user, or log it.

Response - Error Status

  • HTTP status code of 4XX or 5XX
  • Content-Type header of application/json
  • The server SHALL return a FHIR OperationOutcome resource in JSON format

Note: Even if some of the requested resources cannot successfully be exported, the overall export operation MAY still succeed. In this case, the Response.error array of the completion response body SHALL be populated with one or more files in ndjson format containing FHIR OperationOutcome resources to indicate what went wrong (see below). In the case of a partial success, the server SHALL use a 200 status code instead of 4XX or 5XX. The choice of when to determine that an export job has failed in its entirety (error status) vs returning a partial success (complete status) is left up to the implementer.

Response - Complete Status

  • HTTP status of 200 OK
  • Content-Type header of application/json
  • The server MAY return an Expires header indicating when the files listed will no longer be available for access.
  • A body containing a JSON object providing metadata, and links to the generated bulk data files. The files SHALL be accessible to the client at the URLs advertised. These URLs MAY be served by file servers other than a FHIR-specific server.

Required Fields:

Field Optionality Type Description
transactionTime required FHIR instant indicates the server's time when the query is run. The response SHOULD NOT include any resources modified after this instant, and SHALL include any matching resources modified up to and including this instant.

Note: To properly meet these constraints, a FHIR Server might need to wait for any pending transactions to resolve in its database before starting the export process.
request required String the full URL of the original bulk data kick-off request
requiresAccessToken required Boolean indicates whether downloading the generated files requires a bearer access token

Value SHALL be true if both the file server and the FHIR API server control access using OAuth 2.0 bearer tokens. Value MAY be false for file servers that use access-control schemes other than OAuth 2.0, such as downloads from Amazon S3 bucket URLs or verifiable file servers within an organization's firewall.
output required Array an array of file items with one entry for each generated file. If no resources are returned from the kick-off request, the server SHOULD return an empty array.

Each file item SHALL contain the following fields:

- type - the FHIR resource type that is contained in the file.

Each file SHALL contain resources of only one type, but a server MAY create more than one file for each resource type returned. The number of resources contained in a file MAY vary between servers. If no data are found for a resource, the server SHOULD NOT return an output item for that resource in the response. These rules apply only to top-level resources within the response; as always in FHIR, any resource MAY have a "contained" array that includes referenced resources of other types.

- url - the path to the file. The format of the file SHOULD reflect that requested in the _outputFormat parameter of the initial kick-off request.

Each file item MAY optionally contain the following field:

- count - the number of resources in the file, represented as a JSON number.
error required Array array of error file items following the same structure as the output array.

Errors that occurred during the export should only be included here (not in output). If no errors occurred, the server SHOULD return an empty array. Only the OperationOutcome resource type is currently supported, so a server SHALL generate files in the same format as bulk data output files that contain OperationOutcome resources.
extension optional JSON Object To support extensions, this implementation guide reserves the name extension and will never define a field with that name, allowing server implementations to use it to provide custom behavior and information. For example, a server may choose to provide a custom extension that contains a decryption key for encrypted ndjson files. The value of an extension element SHALL be a pre-coordinated JSON object.

Example response body:

  {
    "transactionTime": "[instant]",
    "request" : "[base]/Patient/$export?_type=Patient,Observation",
    "requiresAccessToken" : true,
    "output" : [{
      "type" : "Patient",
      "url" : "http://serverpath2/patient_file_1.ndjson"
    },{
      "type" : "Patient",
      "url" : "http://serverpath2/patient_file_2.ndjson"
    },{
      "type" : "Observation",
      "url" : "http://serverpath2/observation_file_1.ndjson"
    }],
    "error" : [{
      "type" : "OperationOutcome",
      "url" : "http://serverpath2/err_file_1.ndjson"
    }],
    "extension":{"http://myserver.example.org/extra-property": true}
  }

File Request

Using the URLs supplied by the FHIR server in the Complete Status response body, a client MAY download the generated bulk data files (one or more per resource type) within the time period specified in the Expires header (if present). If the requiresAccessToken field in the Complete Status body is set to true, the request SHALL include a valid access token. See the Security Considerations section above.

The exported data SHALL include only the most recent version of any exported resources unless the client explicitly requests different behavior in a fashion supported by the server (e.g. via a new query parameter yet to be defined). Inclusion of the .meta information is at the discretion of the server (as it is for all FHIR interactions).

Example NDJSON output file:

{"id":"5c41cecf-cf81-434f-9da7-e24e5a99dbc2","name":[{"given":["Brenda"],"family":["Jackson"]}],"gender":"female","birthDate":"1956-10-14T00:00:00.000Z","resourceType":"Patient"}
{"id":"3fabcb98-0995-447d-a03f-314d202b32f4","name":[{"given":["Bram"],"family":["Sandeep"]}],"gender":"male","birthDate":"1994-11-01T00:00:00.000Z","resourceType":"Patient"}
{"id":"945e5c7f-504b-43bd-9562-a2ef82c244b2","name":[{"given":["Sandy"],"family":["Hamlin"]}],"gender":"female","birthDate":"1988-01-24T00:00:00.000Z","resourceType":"Patient"}

Endpoint

GET [url from status request output field]

Headers

  • Accept (optional, defaults to application/fhir+ndjson)

Specifies the format of the file being requested.

Response - Success

  • HTTP status of 200 OK
  • Content-Type header that matches the file format being delivered. For files in ndjson format, SHALL be application/fhir+ndjson
  • Body of FHIR resources in newline delimited json - ndjson or other requested format

Response - Error

  • HTTP Status Code of 4XX or 5XX

More Information

You can’t perform that action at this time.